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ABSTRACT:
PROVIDER: PRJNA811332 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:10 DeNovo assembled rice genomes
| PRJEB51974 | ENA
Project description:With the availability of a high quality draft rice genome sequence, large mutant collections, and gene expression oligo arrays for rice, we are now well positioned to dissect rice defense pathways. To do this, we performed global expression analyses to identify genes that are differentially expressed in 10 mutant lines (i.e., Xa21, NH1ox, NRR1ox, GR978, spl11, spl17, NBS2-PI9ox, MPK5ox, OsCoi1ox, and OsNahG1ox), exhibiting altered defense responses. As controls, we used wild typle varieties same with these mutants. Keywords: disease response
2008-05-10 | GSE9653 | GEO
Project description:Nucleosome positioning dictates the DNA accessibility for regulatory proteins, and thus is critical for gene expression and regulation. It has been well documented that only a subset of nucleosomes are reproducibly positioned (phased) in eukaryotic genomes. The most prominent example of phased nucleosomes is the context of genes, where phased nucleosomes flank the transcriptional starts sites (TSSs). It is unclear, however, what factors influence nucleosome phasing in regions that are not close to genes. We performed a combinational mapping of nucleosome positioning and DNase I hypersensitive sites (DHSs) across the rice genome. We discovered that DHSs located in a variety of contexts, both genic and intergenic, were flanked by strongly phased nucleosome arrays. Our results support the barrier model for nucleosome organization as a general feature of eukaryote genomes, including plant genomes, and not limited to TSSs. Specifically, regions bound with regulatory proteins, including intergenic regions, can serve as barriers that organize phased nucleosome arrays on both sides. Our results also suggest that rice DHSs often span a single, phased nucleosome, similar to the H2A.Z-containing nucleosomes observed in DHSs in the human genome. We propose that genome-wide nucleosome positioning in the eukaryotic genomes is orchestrated by genomic regions associated with regulatory proteins. Rice chromatin was digested by micrococcal nuclease (MNase) into mono-nucleosome size. Mono-nucleosomal DNA was isolated and sequenced (MNase-seq) using Illumina sequencing platforms. We obtained a total of 38 million (M) single-end reads from our first MNase-seq experiment and mapped ~26 M to unique positions in the rice genome. We also conducted pair-end sequencing of an independent MNase-seq library, obtained 274 M paired-end reads, and mapped ~231 M read pairs to unique positions in the rice genome.We applied a strategy of combinational mapping of nucleosome positioning and DHSs (GSE26610) to examine whether nucleosome positioning is associated with all cis-regulatory elements in the rice genome. All datasets used in the analysis were developed using rice leaf tissue in the same developmental stage
2014-05-01 | E-GEOD-53027 | biostudies-arrayexpress
Project description:This study aims to deal with a comparative proteome analysis of shoot and root tissues of contrasting phosphorus (P) responsive rice genotypes (Pusa-44 and its near-isogenic line (NIL)-23 harboring Pup1 QTL). Proteins were isolated from shoot and root tissues collected from 45-day-old rice plants grown hydroponically in PusaRicH medium with P (16ppm, +P) or without P (0 ppm, -P) under controlled environmental conditions. Following protein quantification using the Bradford method, and quality check using 1D SDS-PAGE, trypsin was used for in-solution digestion and Nano ACQUITY UPLC-MS/MS was used to separate and identify peptides. This study aimed at deciphering the molecular aspect of Pup1 QTL in P-starvation stress tolerance in rice.
2023-02-27 | PXD039084 | Pride
Project description:This project aims to analyze rice plasma membrane proteins related to resistance against rice blast infection. We extracted rice plasma membrane proteins before and after M.oryzae infection for 24h, and then used trypsin to digest and iTRAQ to label the peptides, HPLC-MS/MS was used to seperate and identify peptides. 1.1/0.909 fold change with p-value < 0.05 was used as threshold for differentially expressed proteins. 2,977 proteins were identified and 951 of which were found to be responsive to resistance against M. oryzae. Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and protein interaction network showed that plenty of proteins were involved in vesicle trafficking with obvious functional tendencies towards transport, vesicle-mediated transport, secretion, endocytosis and phagosome. 10 DEPs were validated at transcript level, and a SNARE protein named NPSN (novel plant-specific SNARE)13 actively responded to M. oryzae infection, and it contributed to rice blast resistance and mainly located at PM.
2022-05-19 | PXD028545 | Pride
Project description:The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing either ABA or GA (Gibberellin) plant hormones and cultured for 3 d. The concentration of the plant hormone was adjusted to 50 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was amplified, labeled, and hybridized to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer. Keywords: other
2004-03-05 | GSE661 | GEO
Project description:Yield and quality are the two most important traits in crop breeding. Exploring the regulatory mechanisms that affect both yield and quality traits is of great significance for understanding the molecular genetic networks controlling these key crop attributes. Expansins are cell wall loosening proteins that play important roles in regulating rice grain size. We investigated the effect of OsEXPA7, encoding an expansin, on rice grain size and quality. OsEXPA7 overexpression resulted in increased plant height, panicle length, grain length, and thousand-grain weight in rice. OsEXPA7 overexpression also affected gel consistency and amylose content in rice grains, thus affecting rice quality. Subcellular localization and tissue expression analyses showed that OsEXPA7 is localized on the cell wall and is highly expressed in the panicle. Hormone treatment experiments revealed that OsEXPA7 expression mainly responds to methyl jasmonate, brassinolide, and gibberellin. Transcriptome analysis and RT-qPCR experiments showed that overexpression of OsEXPA7 affects the expression of OsJAZs in the jasmonic acid pathway and BZR1 and GE in the brassinosteroid pathway. In addition, OsEXPA7 regulates the expression of key quantitative trait loci related to yield traits, as well as regulates the expression levels of BIP1 and bZIP50 involved in the seed storage protein biosynthesis pathway. These results reveal that OsEXPA7 positively regulates rice yield traits and negatively regulates grain quality traits by involving plant hormone pathways and other trait-related pathway genes. These findings increase our understanding of the potential mechanism of expansins in regulating rice yield and quality traits and will be useful for breeding high-yielding and high-quality rice cultivars.
2024-06-30 | GSE256331 | GEO
Project description:Intestinal explants from 5-weeks old piglets were exposed 4h to control or 10 µM deoxynivalenol-contaminated cell culture medium. Explants were nitrogen frozen. RNA were extracted, quantified and their quality was checked with Tapestation 4200 device. RNA samples were used to perform a microarray experiment
2021-06-30 | GSE165968 | GEO